Bowman started his directorial career in television with an episode of Stingray at the age of 26, and has never looked back. Brought in by producer Robert Justman to direct the Star Trek: The Next Generation episode "Where No One Has Gone Before" as a replacement for Daniel Petrie, he went on to become one of the most important directors in the show's first two seasons. He directed his last episode in 1990, having helmed thirteen episodes in all.

Justman considered bringing the young Bowman to the show one of his proudest achievements in The Next Generation. Bowman was terrified at first, trying to make a good impression and overcome any doubts regarding his age. (Star Trek: The Next Generation Companion, p. 36) Producer Rick Berman accidentally mistook Bowman for the pizza delivery guy when he first reported for work. [1]

Following his work on Star Trek, Bowman directed episodes of Alien Nation, Booker, Manucso F.B.I., Baywatch, The Young Riders, and In the Heat of the Night. Besides his X-Files work, Bowman directed numerous episodes of television series such as Day Break and Castle. He also directed a few feature films, mostly science fiction and action projects, such as Reign of Fire (2002, with Alexander Siddig and Alice Krige) and Elektra (2005, with Cary-Hiroyuki Tagawa).

Wil Wheaton has stated about directors, "most of them favored grabbing me by the elbow and moving me around the set, rather than, you know, giving me direction like I was a person or a professional or anything like that. ... but Rob Bowman, who directed this episode "Where No One Has Gone Before", actually treated me really well." and "Rob Bowman directed me to be as mature as I was capable of being when I was just 14." [2]